Struggling Emotions
by Spirit Charmer
Summary: Athrun succeeded in capturing the Strike and tries to convince Kira to stay with him in Zaft. But...will Kira's feelings for the crew back at the Archangel over power the feelings he holds for Athrun? AThrunxKira


**Title: Struggling Emotions**

**Pairing: Athrun x Kira**

**Summary:**What would've happened if Athrun had succeeded in capturing the Strike? Would Kira's feelings to protect the Archangel prove more important that his feelings for Athrun?

**Warning: **Do I have to say that this is Yaoi? Yes, it involves two boys kissing and many other things. If you feel uncomfortable with this sort of thing, then hit that back button right now. Don't expect me to react to flames, I just ignore them, but I welcome those lovely reviews. Enjoy the story.

**Disclaimer: I do not own Gundam Seed, Athrun, Kira, or anything else. So, please don't sue me, I'm seriously not worth it.**

**Struggling Emotions****

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Kira was alone in the Strike's cockpit in an unfamiliar territory. He was captured by the Aegis and was now surrounded by the enemy. In the battle before, Mwu's mobile armor was damaged severely. Kira watched helplessly as the Archangel rushed to retrieve it. His Phase Shift went down, and the Aegis came up from behind the Strike, locking on to it. The last thing he remembered from that was Mwu telling him to bear whatever is to come; he will be rescued in no time at all.

'Sure' he thought, 'If the Archangel had come to rescue me, then Mwu wouldn't be alive…but how are they going to rescue me here?' A tear rolls down his smooth cheek. 'I wonder…if everyone will be alright…' Slowly curling up into a ball, Kira's sobs are the only thing he can hear.

"What was the point in capturing him?"

Yzak's eyes pierced through Athrun giving him an uncomfortable feeling. Despite that, his face was still holding a steady gaze as if he was unaffected. "Because we can use him, he's a coordinator too!" Athrun retorted.

Nicol and Dearka were both staring at their comrades in the most interest. "What makes you think he will help us? He's a traitor who's been fighting for the Earth Alliance!" Yzak was clearly getting more and more angry as each moment passed by.

Of course he was furious at Athrun for defying orders and going to capture the Strike. They already had four of the mobile suits; there was no need for the fifth with a pilot who had fought along side with their enemy. "He will join up with us. I'm going to make sure of that." Athrun's brilliant jade eyes held a distinct determination as he stood his ground.

"And if he doesn't?" Yzak took a step closer to the Aegis pilot. "What are you going to do him if he refuses? Take him back to where you found him?"

Athrun took a slight step back, still holding up his determination to convince the silver-haired pilot without giving him any hints about his relationship with Kira. As far as he knew, neither Yzak, Nicol, or Dearka knew about the fact he grew up with the boy. He wanted to keep it that way for the time being.

"It won't come to that, he will join up with ZAFT, no matter what you think." Athrun slowly walked past the silver haired boy and out the door towards the garage.

As Athrun walked down the corridor, he could hear shouts coming from where the Strike was being held. From what he could tell, they were directed at Kira, ordering him out of the Strike. Athrun quickened his pace to see what was going on. There were several men getting ready to force the cockpit open, and others standing by to retrieve the pilot.

'They are acting like he's a wild animal or something!' Athrun thought to himself as he went up to the first man that was closest to him. "Have everyone leave here immediately, leave the pilot where he is." Athrun's voice was firm in order to show his authority.

The man gave him a slight glare before he replied. "We have orders to retrieve the pilot and take him to the bridge as soon as possible. For what reason must we leave?"

Athrun's eyes had a cold glimmer as he spoke. "I will retrieve the pilot, but I want no one to be in here for when I do it. Now have everyone leave immediately." Athrun stood tall to make himself seem a bit more intimidating. From what he could tell, it worked. The man nodded in an agreeable manner as he turned to the other men. After giving a sharp whistle, which made Athrun shudder, all the men in the garage left in a civilized order.

As soon as everyone was gone, he made his way up to the door to the cockpit on the Strike. "Kira…? Are you in there?"

Athrun's voice became much softer in order to soothe his friend from getting frightened. 'Knowing him, he's probably crying…but this was the only way I could get him to come here.' After waiting for a few moments, Athrun got no answer from the boy inside the mobile suit. Thinking that he spoke too softly, Athrun gave a slight bang and called Kira's name again.

"What do you want?" Kira's voice was muffled from pressing his face too close to his body. There was a clear tone of anger in voice as well as the evidence of him crying.

Athrun took a deep breath as he spoke again. "Kira…why don't you come out here? Nothing will happen to you."

His voice had a ring of softness. Kira perked up a bit, but when he thought about his situation, he gave him a sharp "No."

Athrun moved in front of the door, and sat down about a foot away from it. 'Most likely, this might take a while.' He put his right hand on the door and felt the coolness of the metal seeping through his gloved hand. His green eyes closed slowly as he began to think about how he would be able to convince his childhood friend to come out. "Why won't you come out, Kira…? Don't you remember that I'm your friend?"

Kira never thought he wasn't his friend. He raised his head a little from his knees. "I never said anything like that. I know you're my friend. I never thought you weren't. It's just…how am I supposed to believe there is no one out there ready to kill me or something?" Kira's shoulders began to shake with fright.

Athrun had a slight look of shock on his face from what his friend had just said. 'Does he…not trust me?' Then again, he is in enemy territory, its only natural to think that.

Athrun scooted a little closer. He was not going to just leave his friend in there. Kira wouldn't want several men to force that door open and rip him out of there. 'No…he's too fragile for that, I wouldn't be able to bear it if that happened to him.' He placed his hand in his lap as he opened his mouth to speak again. "I promise, Kira. I will protect you, no one is going to hurt you. Besides, it's safer with me than in there all alone. You can't possibly survive in there for very long."

Athrun's voice held a sharp tone of determination. He wanted Kira to know that no one would even touch him, and he would make sure of that.

"You forget, Athrun…I'm also a coordinator. I can survive in here a lot longer than a natural without food." Though his voice also sounded determined, it was obvious that Kira was scared of being left alone. 'What should I do…I want to go out there with Athrun, but what if he can't protect me? What will happen?'

After several moments of silence, A sharp sound was heard from outside, Kira could've probably jumped straight through all of the metal plating from shock. "ATHRUN! What's going on?"

Fear was overwhelming the young boy's body and mind. Slight bangs could also be heard as if someone was trying to force the door open.

"I'm sorry, Kira. But from the way I see it, I won't be able to convince you to come out of there." Athrun sounded a little strained from his activities. From what he could hear, Kira knew Athrun was probably doing this by himself.

After giving it a quick thought, Kira opened the door. Athrun fell right on top of Kira with the crowbar he was using falling at their sides. Shocked green eyes met teary amethyst ones, their noses almost touching. A small blush appeared on both boys' faces, as Athrun quickly got up from Kira and out of the cockpit.

Wiping the sweat from his forehead, the Aegis pilot stretched out a hand for the Strike's. Kira looked long fully at the hand that was offered to him, then managed to grab it carefully. The blue haired boy pulled the other boy out and close to him. Again, their faces got extremely close to touching the other. Both scooted away from the other slightly with a small pink blush on both of their faces.

"Well, I'm glad you decided come out finally." Athrun said with a light-hearted chuckle.

Kira smiled at his friend as he looked around the entire garage. It seemed so awkward for him to be standing where he was. "What are you going to do with me? I would think that I'm your prisoner." Kira asked full of concern.

The azure haired boy gave the brown haired one a warm smile before putting a hand on his shoulder. "You may be my prisoner, but I will make sure you aren't treated like one. C'mon, let's get out of here." Athrun turned and started walking down the steel stairs and towards the door.

Kira quickly walked to catch up with him and walked side by side. Athrun looked at Kira with a concerned look as he pulled a gun and put it to his back. "Wha…what?"

Amethyst eyes whirled to stare at the other's face in fear. Looking down at him with sharp eyes, Athrun leaned in close. "Don't worry, we'll just walk like this until I get you to my room. It will be suspicious otherwise."

The two continued to walk down the corridor, passing a few crewmembers. When Athrun stopped abruptly, he looked at Kira with kind eyes as he opened the door in front of him. Slowly they both walked in, it was a plain room with two beds, two dressers, and a desk in the corner. The desk had various parts and unfinished Haros. The two dressers were on either side of the beds for clothes or whatever. Athrun led Kira over to one of the beds and sat him down.

"I will go to the bridge and request that you stay here instead of the prison block. It shouldn't be a problem, even though I share this room with Nicol. Make yourself at home for now." Athrun gave him a slight smile before leaving.

Amethyst eyes wandered around the room, and then to the floor. 'I wonder how everyone is doing right now…I hope the Archangel is safe…' The boy got up and walked over to the desk, looking down at the pieces and half-finished Haros, and smiled. 'It seems Athrun hasn't changed much at all. He still likes building these micro units…I never understood those things…' His eyes wandered the desk a bit more and then stopped when he spotted a picture. "Wha…? This is…Athrun and me…"

The picture had a young Athrun and Kira playing together. They looked around eleven or twelve or maybe even thirteen. Both of them had their arms slinked over the other's shoulder. Kira smiled at the photo as he thought about that time. From behind him, the door opened and Kira quickly turned around.

"You okay? I just talked to Commander Creuset; it's all right for you stay here for now. You don't have to worry about anything." Athrun's eyes turned from Kira's face to the picture that was still in his hand. Looking back at him, he gave Kira a soft smile.

The blue haired boy walked over to the brown haired one. Kira's eyes widened a bit when Athrun got really close to his face. He felt the picture being taken from his hand. Athrun looked at it with a dreamy look on his face as he went to put it back on the desk. "Three years…it's been three years since I left for Plant. In a way, it doesn't feel that long."

Kira looked at Athrun with a confused face, it made him look absolutely adorable. "It doesn't feel like three years? It felt like longer for me, Athrun…without…you."

Athrun perked up a bit before looking at Kira with a shocked look. His green eyes glittered as a small blush rose onto his cheeks. The Strike's pilot was looking down at his feet to hide his blush.

After an awkward moment of silence, Athrun gathered up his courage and embraced the other boy. Out of shock, Kira froze in place before relaxing into the warmth. "Kira…have you really been that lonely for all this time?"

Kira's body tensed as he tried to find the words to either deny or confirm what Athrun had just said. Athrun's mind had just kicked in when he realized what he had just done. Quickly releasing the other boy, he walked a few steps away from Kira. Mixed feelings of regret and sorrow welled up in the pit of Athrun's stomach. Wrapping his arms around himself, Athrun let out a sigh as he turned to face Kira. Kira was looking down at the floor as if he was trying to think of what to say. When Athrun opened his mouth to apologize, Kira cut him off. "Yes…I couldn't stand being apart from you…So many days…I just wished I could see you again…"

Tears began to stain the smooth skin on his face while some fell onto the floor near his feet. Short sniffles could be heard from the older boy. Athrun took a step forward and held out his hand. The whimpering boy looked up and grabbed the younger boy's hand and held it close to his mouth, kissing it gently. Taking this as a sign, Athrun walked closer and embraced the boy yet again. This time Kira responded by wrapping his arms around him.

The younger boy buried his face into the older boy's hair, inhaling the sweet scent and pulling him into a tighter embrace. When Kira began to shift a little, Athrun loosened his hold and stared deeply into amethyst pools. The brown haired boy looked in to the others eyes full of emotion.

Athrun smiled warmly and softly pressed his lips against Kira's. Kira's eyes widened a bit from the shock, but relaxed into the kiss. Athrun pulled away to look at his dear friend. Kira looked at him with a mixture of contentment and love. There was something else he saw in his eyes, what looked like…lust?

Athrun pressed his lips a bit firmer this time to Kira's as he shifted them to push Kira onto one of the beds. Upon falling on his back with Athrun, Kira let out a small yelp. The blue haired pilot looked down at Kira with concern and then pulled him into another passionate kiss. Kira gasped when he felt a soft wetness brush across his lips. Athrun took this opportunity to thrust his tongue into the older boy's mouth. The Strike's pilot's eyes widened upon this intrusion, but allowed the other pilot to explore the territory of his mouth.

When Athrun pulled away, sopping up the taste of his desire, he began to undo the upper part of Kira's blue and white suit, but stopped at the belt. Kira sat up to help him get his arms out of the sleeves. As soon as Kira's arms were free, Athrun continued down to undo the rest of the suit. The blue haired boy began to make a trail of sloppy kisses starting from Kira's jaw line down to one of his hardening nipples. Kira gave out soft moans and whimpers as the younger boy was suckling.

The brown haired boy's back arched when the other boy switched to give the other one the same treatment. Athrun went back up to give the older boy another passionate kiss as his hand started going lower and lower.

Kira gave a long moan when he felt Athrun's fingers ghost over his hardness. His back arched as Athrun continue his journey downward. When he felt the warm breath trickle over his tip, Kira's hands started grabbing the sheets around him helplessly. Athrun's warm tongue began to draw lazy circles around the tip and then slipping into the slit at the top, receiving several other moans. Dark amethyst eyes shot open when the feeling of being engulfed enveloped his body.

The paler boy was swirling his tongue around the hard shaft that was in his mouth, ignoring the fact that his own arousal is pressing against the fabric of his red and white suit. Hands were pulling at his blue hair, causing slight pain. Kira however didn't realize this, being too lost in pleasure. Athrun then began to create a vacuum motion and humming softly to create more friction. The boy above him was writhing uncontrollably, tearing at the sheets around him and at his own azure locks. As soon as Athrun began bobbing his head up and down, Kira's eyes shot open and screamed out his love's name as he released his orgasm into the waiting mouth.

The blue haired boy swallowed as much as he could, some dribbling from his mouth. When he pulled himself up to lie atop of the spent boy, the aching feeling in his groin made him groan. Kira immediately sat up.

"Athrun…" Athrun gave Kira a loving smile as he kissed his passionately. The pilot of Aegis began to undo his own clothes, until they lay strewn across the floor along with Kira's.

"Kira…do you mind?" Athrun's eyes were dark with lust, when Kira saw this; he nodded for him to continue.

Kira closed his eyes, while Athrun began to lubricate three of his fingers with what was left of Kira's release. When he began to reach for the opening, Kira began to open his eyes. The first finger was slowly pushed into Kira, the older boy squirmed in discomfort, but did not force the intruding finger out. After the second finger, Kira winced a bit, but still remained calm. Athrun eyed the boy carefully as he thrust the third finger deep into the other boy, his fingers doing a scissor motion to stretch Kira enough for him to fit without much pain. Athrun removed his fingers, and positioned himself in front of Kira's opening.

Leaning over him, Athrun planted a kiss on the corner of Kira's mouth as he thrust deep into him. Streams of tears and a heart-breaking scream came from Kira; the blue haired boy licked away the tears and planted a kiss on top of his head in attempt to soothe the sobbing boy. Once Kira had stopped crying and he felt the muscles shift to get used to having someone inside of him, Athrun began to thrust. He started off at a slow and steady rhythm, gritting his teeth. Kira put his arms around Athrun's neck and wrapped his legs around his waist.

Athrun continued thrusting into the smaller boy, his movements growing in speed and power. Before long, they were both panting and moaning in rhythm. The pale boy reached between their bodies and wrapped his hand around Kira's hardness and began pumping in time with his movements. With both movements of friction, it wouldn't be long before Kira reached his climax.

Yelling his lover's name, the brunette boy exploded on both of their stomachs and Athrun's hand. The muscles tightening around Athrun increased the friction around his member. In one last thrust, he spilled his seed deep in Kira, crying out his name.

Athrun pulled out of Kira to lie beside his spent partner. He reached over to brush the brown bangs away from Kira's face and planted a chaste kiss on his forehead. The blue haired boy wrapped his arms around the boy next to him to cradle him. Resting his head on top of Kira's, Athrun drifted off to sleep.

Amethyst eyes opened and wandered around the room when Kira awoke. 'Oh that's right…I forgot I'm not on the Archangel.'

He looked down to see not only himself, but also Athrun, naked. Athrun was curled up, resting his head on the older boy's chest, sleeping. Kira shifted a bit, trying to remember what caused them to end up in this awkward position. The recollections of the night before began to come back into Kira's mind. Shocked at what he did, Kira sat up abruptly, accidentally waking up the boy next to him.

"Mmm…wha…? Good morning, Kira." Athrun said sleepily with a smile. Kira smiled back and got up to put back on his clothes. Athrun sat up and stared, "Is something wrong?"

Kira looked behind him with a smile. "No, nothing is wrong…only…I'm just wondering about everyone back on the Archangel…"

The sadness was clear in his tone, Athrun noticed this. From what it seemed, Kira wanted to go back to the Archangel rather than stay here with him. He didn't want to lose him again. "Kira…why don't you stay here? This is where you belong, with other coordinators."

Kira looked back at him with sadness in his eyes. As he zipped up the zipper on the front of his blue and white suit, he turned to face the boy. "Athrun…I…can't…There are people on that ship that I promised to protect. Besides, I don't want to be part of this war."

The blue haired boy moved over to one of the small dressers and took out one of his red and black ZAFT uniforms. As he began to get dressed, he looked over at Kira, who was staring at the floor. Athrun turned around and directed his intense gaze towards the other boy. "You don't realize what's going on, do you?"

Amethyst pools stared into the captivating green eyes of the other boy. He walked closer to the ZAFT soldier and stood in front of him.

"Going on? What's going on?" Kira's face showed sheer curiosity for what his friend was asking him. He didn't know there was anything going on. He stepped a bit closer. "Athrun…what do you mean?"

Athrun finished putting on the red coat and stared deeply into Kira's eyes. "How can you be so naïve? The naturals are just using you for their own personal gain. You are nothing, but a weapon to

them. They only worry about you because without you and the Strike, they have already lost this war!" Athrun's face and voice were dripping with bitterness when he said that. His normally warm eyes that he showed when he looked at Kira had turned to ice. The way he was looking at the boy seemed to make Kira feel as if he was shrinking.

"That's not true! My friends are on that ship!" Kira's features growing immensely sharp and bitter. He narrowed his eyes, giving Athrun a cold glare.

"Friends? How can you be friends with naturals? Kira! Don't you realize, I want you to be safe! I want to protect you! I want to…be with you." The blue haired boy walked up to Kira and embraced him tightly.

The other boy rested his head on younger one's shoulder, as he wrapped his arms around him. Tears beginning to stream down his face and he buried his eyes into the other's shoulder. Athrun rested a hand on the back of Kira's head, as if to cradle him. "I'm sorry Athrun…but I have to go back…"

"Kira…" A sigh escaped from Athrun's lips as he looked up at the ceiling. When he looked back down at the boy in his arms, he pulled back and smiled softly. Athrun planted a soft, loving kiss on Kira's lips and nodded to show his understanding. After pulling away from Kira, Athrun walked towards the door. "I'm going to make sure there are no people to see this, alright? I want you to go down to where the Strike is and get it ready for launch. When I give the signal, leave Kira. Do you understand?"

Athrun's eyes had a determined, but sad look to them. When Kira gave the nod, the ZAFT soldier left to walk down where the Strike was held. Aside from a few crew workers, there were no people guarding it. Going up to the nearest one, he asked for them all to leave immediately. When the garage was empty, Athrun went back to his room to get Kira.

"Go to your mobile suit, and get it ready. Afterwards launch out of here." Athrun's voice was urgent, and commanding. Kira looked at him with concern before embracing him one last time.

"But…what will happen to you?" Kira tightened his embrace. "I don't want anything bad to happen to you, Athrun…"

Athrun pulled away and looked into his eyes. "Don't worry, I'll be fine. Go Kira!"

As soon as he was told, Kira hurried down the corridor and into the Strike. After a few moments of preparing, the Strike launched into space and away. Alarms went off, and Athrun walked over to his desk and picked up the picture of him and Kira and smiled. "Enemies once more…"

**End**

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A/N: **First Fanfic I ever wrote, but I fixed up the paragraph construction. What the heck was I on when I wrote this, I couldn't even figure out who was saying what! xDD Sorry, everyone! 


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